I would think they should go on the intake side so the water has to run through the cylinder to get out, otherwise if its on the exhaust side, the water can short circuit right through the front of the cylinder without really circulating through the rest of the waterjacket.

We are sorry, but we do not have instructions for the 785 Pro head. But,
the water outlets should be on the intake side, that way the water flows
across the cylinders and head. With the one piece head shell, the head is
open and does not direct the water flow like a cast or 2 piece head. All 3
outlets need to run to the water block, which provides equal flow to all 3
cylinders.